Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

Integrative analysis workshop with TCGAbiolinks and ELMER

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

Context-sensitive creation of kinetic equations in biochemical networks

doRiNa - database of posttranscriptional regulatory elements

MSLCRN: a novel step-wise method for inferring module-specific lncRNA-mRNA causal regulatory network in human cancer

CMTCN: A web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks

A package that ranks the SNPs using genomic, epigenomic and network based features.

Statistical Inference for Network Centrality

ASP-based attractor computation

Supplemental scripts and analyses for the SINGE manuscript

Hub and Spoke Landing Zone for either Azure Commercial or Azure Government scenarios.

Reconstruct a Transcriptional Regulatory Network using the principle of Maximum Entropy.

A novel insight into neurological disorders through HDAC6 protein-protein interactions

Python Implementation of PROM

A minimal Python library for gene regulatory network inference.

Identification and classification of network fibers for general information networks. (C/Python)